On 2011-09-29, at 7:58 PM, Peter Cock <p.j.a.cock(a)googlemail.com&gt; wrote: > On Thu, Sep 29, 2011 at 7:49 PM, Cecilia Tamborindeguy > <ctamborindeguy(a)ag.tamu.edu&gt; wrote: >> Hello, >> >> I would like to know if Galaxy can do de novo assembly without a reference >> genome. >> >> Thanks. >> >> Cecilia > > Are you trying to use the Public Galaxy or a local install? There > are several assemblers with Galaxy Wrappers on the Galaxy > ToolShed (e.g. Roche "Newbler", and MIRA 3) which you could > add to your own local Galaxy if you have one. > > However, do novo genome assembly can be very computationally > demanding, so not many Galaxy Instances will want to offer it. > > Peter I would like to echo Peter's advice. (Again, that's twice in 5 min from 2 different lists. I promise you I'm not stalking you, Peter). Genome assembly is a bit of a dedicated domain with respect to expertise and time. If possible, if you are assembling a lot of genome data, you really should set yourself up properly with a multiple-CPU unix box with a lot of RAM and dedicate it to assembly. Install MIRA, Newbler, Velvet, AMOS, samtools, bamtools, bedtools, Staden, phred/phrap/consed on it, and you can assemble and interconvert data to your heart's content. Galaxy is a wonderful and useful service but assembling genomes does require dedicated power and expertise, and preferably in house. I just forked out for a 64 CPU processor with 1 TB RAM bc we assemble lots of genomes. You don't have to go that far but a 3-4 quad processor box with 128 GB RAM and 1 TB disk should be on your mind. John